[BUG] compute_shape_offset triggers PyTorch ≥2.9 breaking change for non-tuple sequence indexing

[AryanMoradi]

Describe the bug

compute_shape_offset in monai/data/utils.py (line 883) passes spatial_shape directly to np.array(). When spatial_shape is a PyTorch tensor, this triggers the non-tuple sequence multidimensional indexing deprecation that became a breaking change in PyTorch 2.9+.

To reproduce

Run any pipeline that goes through SaveImaged → NiftiWriter.set_metadata → resample_if_needed → spatial_resample → compute_shape_offset with PyTorch ≥ 2.9.

Expected behavior

No error. spatial_shape should be converted to a plain Python tuple before being passed to np.array.

Actual behavior

On PyTorch ≥ 2.9, this either raises an error or produces silently wrong results.
On PyTorch 2.8 it was a deprecation warning.

Environment

• MONAI: 1.5.2
• PyTorch: 2.10.0+cu129
• Python: 3.11
• OS: Windows 11

Suggested fix

# monai/data/utils.py, line 883
# Before:
shape = np.array(spatial_shape, copy=True, dtype=float)
# After:
shape = np.array(tuple(spatial_shape), copy=True, dtype=float)